Genome-wide detection of CNV regions and their potential association with growth and fatness traits in Duroc pigs

Qiu, Yibin; Ding, Rongrong; Zhuang, Zhanwei; Wu, Jie; Yang, Ming; Zhou, Shenping; Ye, Yong; Geng, Qian; Xu, Zheng; Huang, Sixiu; Cai, Guangyan; Wu, Zhenfang; Yang, Jie

doi:10.1186/s12864-021-07654-7

Cited by 29 publications

(25 citation statements)

References 80 publications

(77 reference statements)

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“…CNVs, which usually range from one kilo-base (kb) to several mega-bases (Mb) [ 1 ], were associated in livestock animals with changes in the phenotypic expression of simple traits (such as the presence or absence of horns, [ 2 ]), and also disease susceptibility and genetic disorders [ 3 ]. In addition, recent studies carried out on wildlife and livestock species have pointed to CNVs as a major source of genetic and phenotypic variation among individuals [ 4 , 5 , 6 ]. For this reason, increasing our knowledge of the existence and function of CNVs in livestock, particularly related to complex traits and environmental adaptability, contributes to a greater genetic improvement of economic and production traits and animal health [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

Copy Number Variation (CNV): A New Genomic Insight in Horses

Laseca

Molina

Valera

et al. 2022

Animals

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Copy number variations (CNVs) are a new-fangled source of genetic variation that can explain changes in the phenotypes in complex traits and diseases. In recent years, their study has increased in many livestock populations. However, the study and characterization of CNVs in equines is still very limited. Our study aimed to investigate the distribution pattern of CNVs, characterize CNV regions (CNVRs), and identify the biological pathways affected by CNVRs in the Pura Raza Española (PRE) breed. To achieve this, we analyzed high-density SNP genotyping data (670,804 markers) from a large cohort of 654 PRE horses. In total, we identified 19,902 CNV segments and 1007 CNV regions in the whole population. The length of the CNVs ranged from 1.024 kb to 4.55 Mb, while the percentage of the genome covered by CNVs was 4.4%. Interestingly, duplications were more abundant than deletions and mixed CNVRs. In addition, the distribution of CNVs across the chromosomes was not uniform, with ECA12 being the chromosome with the largest percentage of its genome covered (19.2%), while the highest numbers of CNVs were found in ECA20, ECA12, and ECA1. Our results showed that 71.4% of CNVRs contained genes involved in olfactory transduction, olfactory receptor activity, and immune response. Finally, 39.1% of the CNVs detected in our study were unique when compared with CNVRs identified in previous studies. To the best of our knowledge, this is the first attempt to reveal and characterize the CNV landscape in PRE horses, and it contributes to our knowledge of CNVs in equines, thus facilitating the understanding of genetic and phenotypic variations in the species. However, further research is still needed to confirm if the CNVs observed in the PRE are also linked to variations in the specific phenotypical differences in the breed.

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Section: Introductionmentioning

confidence: 99%

Copy Number Variation (CNV): A New Genomic Insight in Horses

Laseca

Molina

Valera

et al. 2022

Animals

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“…A total of five economic traits were recorded including average daily gain (ADG) at 100 kg, backfat thickness (BFT), loin muscle area (LMA), lean meat percentage at 100 kg (LMP), and total teat number (TTN) ( Supplementary Table S1 ). The two Duroc lines had moderate genetic differentiation without sampling error, and the detailed descriptions of samples and phenotypes can be found in our previous papers ( 29 – 32 ).…”

Section: Methodsmentioning

confidence: 99%

Identification of Homozygous Regions With Adverse Effects on the Five Economic Traits of Duroc Pigs

Wang

Yang

et al. 2022

Front. Vet. Sci.

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Runs of homozygosity (ROH) are widely used to estimate genomic inbreeding, which is linked to inbreeding depression on phenotypes. However, the adverse effects of specific homozygous regions on phenotypic characteristics are rarely studied in livestock. In this study, the 50 K SNP data of 3,770 S21 Duroc (American origin) and 2,096 S22 Duroc (Canadian origin) pigs were used to investigate the harmful ROH regions on five economic traits. The results showed that the two Duroc lines had different numbers and distributions of unfavorable ROHs, which may be related to the different selection directions and intensities between the two lines. A total of 114 and 58 ROH segments were found with significant adverse effects on the economic traits of S21 and S22 pigs, respectively. Serval pleiotropic ROHs were detected to reduce two or multiple phenotypic performances in two Duroc populations. Candidate genes in these shared regions were mainly related to growth, fertility, immunity, and fat deposition. We also observed that some ROH genotypes may cause opposite effects on different traits. This study not only enhances our understanding of the adverse effects of ROH on phenotypes, but also indicates that ROH information could be incorporated into breeding programs to estimate and control the detrimental effects of homozygous regions.

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“…Recently, studies have shown that CNVs have a potentially greater impact than SNPs [ 5 ].Because CNVs involve a large DNA fragment, this has potentially more severe effects, e.g., changing the structure and dose of the gene, resulting in different phenotypes [ 6 ]. A variety of complex traits and diseases can be affected by CNVs in cattle, such as breeding, immunity, muscle growth, and fat deposition [ 7 ]. More recently, researchers have discovered that some CNVs are related to important traits in animals.…”

Section: Introductionmentioning

confidence: 99%

Distribution of Copy Number Variation in SYT11 Gene and Its Association with Growth Conformation Traits in Chinese Cattle

Yang

Yue

et al. 2022

Biology

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Currently, studies of the SYT11 gene mainly focus on neurological diseases such as schizophrenia and Parkinson’s disease. However, some studies have shown that the C2B domain of SYT11 can interact with RISC components and affect the gene regulation of miRNA, which is important for cell differentiation, proliferation, and apoptosis, and therefore has an impact on muscle growth and development in animals. The whole-genome resequencing data detected a CNV in the SYT11 gene, and this may affect cattle growth traits. In this study, CNV distribution of 672 individuals from four cattle breeds, Yunling, Pinan, Xianan, and Qinchuan, were detected by qPCR. The relationship between CNV, gene expression and growth traits was further investigated. The results showed that the proportion of multiple copy types was the largest in all cattle breeds, but there were some differences among different breeds. The normal type had higher gene expression than the abnormal copy type. The CNVs of the SYT11 gene were significantly correlated with body length, cannon circumference, chest depth, rump length, and forehead size of Yunling cattle, and was significantly correlated with the bodyweight of Xianan cattle, respectively. These data improve our understanding of the effects of CNV on cattle growth traits. Our results suggest that the CNV of SYT11 gene is a protentional molecular marker, which may be used to improve growth traits in Chinese cattle.

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Genome-wide detection of CNV regions and their potential association with growth and fatness traits in Duroc pigs

Cited by 29 publications

References 80 publications

Copy Number Variation (CNV): A New Genomic Insight in Horses

Copy Number Variation (CNV): A New Genomic Insight in Horses

Identification of Homozygous Regions With Adverse Effects on the Five Economic Traits of Duroc Pigs

Distribution of Copy Number Variation in SYT11 Gene and Its Association with Growth Conformation Traits in Chinese Cattle

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